Author's Chapter Notes:Crossover with Doctor Who. Spoilers for season 6 of Doctor Who, specifically the Doctor's Wife. Written for auctorial for xover_exchange on Livejournal

When he had stopped to investigate the anomalous readings his TARDIS had detected only six months ago, he had not expected that he might experience his final death. He had been associating with the Doctor for much too long if he was finding himself in the types of situations. He used to be good at avoiding this sort of thing.

The insect-like humanoid smiled widely at him, showing terrifyingly pointy teeth as it held him by the neck against the wall.

"You will surely taste delicious," it hissed, before slamming its palm against his chest.

He screamed in excruciating pain as years of his life were leeched out of him. His breathing grew labored as he aged decades in mere seconds, and the creature groaned in ecstasy as it fed. His lungs rattled as he took slow, deep breaths and concentrated on his internal systems, intentionally slowing down his binary cardiovascular system. His hearts slowed down, and finally stopped before the feeding was complete.

Believing its prey to be dead, the wraith dropped the food to the ground and stalked off before it noticed the tell-tale signs of regeneration. Golden light swirled around the dead Time Lord's body, his aged body regaining a youthful appearance as wrinkled skin pulled taut, only to scatter when a bright white light reached down and pulled. When the light faded, the hallway was empty.

-----

"Why did you Ascend him? He's not even Alterran! This is why we must have rules governing non-interference!"

The woman at the head of the table sighed as the other Ascended challenged her decision. "He has technology even greater than ours, and with it we could succeed in our attempts to drive out the Wraith."

"That's not our fight anymore! We do not interfere with the lives of our brethren or other species; you agreed on that law!" the man on her left demanded.

"Then why not let him die; why bring him to our plane? His ship would have been found when they went to investigate the attack," another Ascended ask, raising her eyebrow in question.

"It seemed like a good idea at the time –" she started.

"Why would that ever seem like a good idea, Chaya? We do not interfere in the lives of others, and to do so may bring the attention of the Ori upon us!"

There was a loud bang as the man at the other end of the table hit his hand against it.

"Silence! While I agree that Chaya has been foolish in her decision, she does have a point. We have been presented with an opportunity. Roma, inform one of our Alterran brethren of what has occurred, and direct them to the abandoned vessel. Our fellow Ascended had already adapted some of our technology to his before his Ascension; with some study, it will be possible to fully convert the vessel to our technology."

"But we are not allowed to –"

"Roma, do not challenge my decision. Chaya, if you make such a mistake again, I will not be so lenient with you. You are dismissed."

The others grumbled in discontent as they left, displeased that their leader was disregarding the laws they had set by assisting in the fight against the Wraith. It may be time to find a new leader.

-----

If he had been able to walk, he would have paced back and forth. As it was, he merely floated back and forth, which was not nearly as satisfying.

He had never asked to be Ascended, and they kept him on strict watch to make sure he didn't attempt to interfere on his species' behalf. He didn't even know what was happening on Gallifrey, so why would he interfere? Every time he tried, he seemed to hit a blank wall, even though he knew that such abilities were within his reach as an Ascended. Also, whenever he tried to follow a specific Time Lord, he either hit against the blank wall, or saw a chameleon arch, a person who appeared to be patched together like Frankenstein's Monster, or a police box that had to be The Doctor's TARDIS. The other Ascended didn't even know what species he belonged to; they were so arrogant that they believed he belonged to a lesser race, one that had probably already been culled years ago.

To be honest, they seemed to be cut from the same cloth as the Time Lords.

They even believed that they could bend Time Lord technology to their will. Oh, his TARDIS, his poor Atlantis, they had ripped her to pieces during their conversion process. She couldn't even travel through time now, although she had managed to find a Rift deep in the ocean on a planet composed primarily of water that she could live off of. He tried to visit her as often as possible, because without his presence in some way she would die.

They even hooked her up to energy modules that kept the Alterran technology functioning. That was all it was good for, really. They hadn't known what they were doing, and what had once been beautiful reds and blues was ripped out and replaced with blue and green crystals, her console torn apart and covered with bare wires like a spider's web. She couldn't even travel through the Vortex anymore, and could only limp across space powered by the energy modules. They'd also added columns and spires, not understanding that she could easily add any room they desired, but instead adding a city to her so that she wore it like a turtle shell.

He dreamt of the day he could return and remove the source of her pain. All he could do now was wait, and prepare for that day to come.

-----

"Doctor, how do you know that you're the last of your kind?" Amy asked, leaning against the console, staring at the small box that had led them to House.

The Doctor was silent for a moment. "It's quiet."

Amy frowned. "What do you mean? They'd call you up for a chat?"

He shook his head, running a hand through his hair. "What do you hear when you listen to the Vortex?"

Amy blinked at this sudden turn in the conversation, before stopping to think. "I hear a song. It's – I can't describe it. But I hear a song."

The Doctor nodded, turning away from her. "You used to hear hundreds of songs in the Vortex. Now, you only hear one. Me."

"Wait, then why did you think that there would be others alive?" she asked.

"Because the Vortex only sings when someone is in it," he said softly, before spinning towards the console with a shout. "Now, Amy, where's Rory? Do you think he'd like to go to the Classimininigans?" He began to dash back and forth around the console, turning knobs and flicking switches, a large smile on his face. "Nice place, very small, very educational, you'd love it! "

"He's still in our bunk. Doctor," Amy paused, "do you miss them?"

The Doctor's fake smile faltered briefly as he paused in his wild dance around the console. "Some of them, yes. The Master, well, the Master's the Master but he was always good for a distraction. The Corsair was always good for a drink, and the Mathematician, well, you could never tell with him. I wonder what happened to him..."

He stopped to think for a minute. There had been no sign of his communication cube, and if he'd been on Gallifrey during the Time Lock he would have been put to work trying to shut it down. What had happened to the Mathematician?

The Doctor shook himself, and forced his smile back into place as he pulled a lever and the TARDIS began to thrum with intent. "Amy, get Rory! We're heading to Classimininigans, home of the Classimininigan Academy!"

-----

The other Ascended were getting nervous. The Tau'ri had discovered one of the Ancients' gateways on their planet, and had managed to send a man offworld. It was only a matter of time before they were able to figure out how to get him back, and then they would be sending expeditions out and exploring the galaxy. Given enough time, they might even discover how to travel to other galaxies – like Pegasus, where the Wraith hunted and their cities lay abandoned, covered in dust.

This meant that they were lying low and setting failsafes to protect their descendents – it was bad enough that the Tau'ri had discovered Heliopolis. They'd managed to break the DHD to prevent Ernest Littlefield from returning to his planet, but that was only a temporary measure.

However, this also meant had they weren't watching him closely, not any more. What little surveillance they had kept on him after millennia had passed was gone.

It was time to find out what the Doctor was doing outside of his police box, and put in some countermeasures to the changes that the Alterrans had made to Atlantis. He also needed to get back into corporeal form, but the others would be on him the second they found him gone, and would take his memories from him. He needed to remember so he could fully restore Atlantis, figure out how to defeat the Wraith, and discover what had happened to the other Time Lords.

-----

Atlantis hummed happily as he walked her halls down to her main console, trailing his hand against her walls. Her cityship shell was beautiful, even though all it amounted to was a glorified parasite. It depended on her to run, using her power to sustain the energy modules that kept her alive and running. The modules were still running, barely, but they would hold up for about another fifty years. Then, they would die, and it would only be a matter of time before Atlantis' systems shut down and she was flooded with water. Her shell would stop functioning, and her with her power being sent to energy modules that could no longer be sustained, it would only build up and form a cascade reaction, killing his beautiful TARDIS. However, this wasn't his concern, not yet, not now when he was still subject to the rules of the Ascended. He wanted to do things on his terms, not theirs. They would know if he tried to make such drastic repairs.

However, the chameleon arch was nearly fixed, and with just a little more tweaking he would be able to readjust the perception filter and make it functional outside of the TARDIS, as well as finish adjusting the device so it would automatically return to the TARDIS console after it was used. That way, with his essence infused in the fob watch, Atlantis would stay alive even without his presence and he would hopefully be able to return and retrieve it once the Stargate Program reached the Pegasus Galaxy.

Then, he would simply need to forge himself a new identity on Earth. Maybe he could be a John or a David.

-----

He glanced at the nearby calendar as he materialized inside the small office, taking note of the date: June 14, 1970. He wasn't quite sure of how he was going to do this, as neither he nor the chameleon arch could modify the humans' memories and insert himself into their lives, so he would have to hope that they adopted him or ensured that he found a good home.

He double checked the chameleon arch before closing his eyes, gritting his teeth as he forced himself to Descend. As his physical body appeared in a flash of white light, he fell to the floor in pain, his breathing labored as golden flashes of light flickered over his body.

He hadn't taken his regeneration into account, as it had not yet finished when he had first Ascended and was intent on finishing what it had once started, but had foolishly assumed that the regeneration process would be complete when he Descended. Instead, he found himself in a race against time while he tried to regenerate into a younger body as well as lock his Time Lord self away with the chameleon arch at the same time.

He could not fail.

He would not fail.

It was too late to turn back now.

John Sheppard, future Air Force pilot and former Time Lord, was born.

With a flash of light, a fob watch then disappeared from next to his unconscious body only to reappear a galaxy away, on top of the console of an abandoned TARDIS.

-----

John woke up with a gasp, pushing back his blankets as he tried to calm down his breathing, already forgetting his dream. Atlantis hummed softly, and he caressed the wall closest to his bed in return.

This was the fourth time this week that he had woken from a dream that he couldn't recall, and each time he was filled with a sense of urgency, a sense that he was being called somewhere. In a place such as Atlantis, such feelings were usually dangerous because they still didn't fully understand the technology.

John stumbled to his feet and ran his hand through his hair, before pulling on his shoes and leaving his room. The sense of urgency nagged at him, throbbing like a sore tooth. He knew he should tell someone, but he couldn't bring himself to inform anyone.

He stumbled down the hall into the nearest transporter, before instinctively selecting an area no exploration teams had yet entered. When the doors to the transporter opened, he stumbled out in shock, staring at the area that looked nothing like the rest of the city that he had seen. There were bare wires everywhere, with connections leading every which way. There was a large dais in the middle of the room with devices attached that he knew were not Ancient in origin, such as that rotary telephone and a strange blue orb that looked like a crystal ball, if crystal balls were the size of a large turkey.

He walked cautiously over, just waiting for something to light up, but the room stayed dark, the only light emitting from the various buttons on what had to be a console of some sort.

There was a fob watch lying on top of it, and it felt like he was outside of his body, looking in, as his hand reached out, carefully held it, and opened it.

A bright light filled his vision, and he couldn't look away even if he wanted to. He heard a song he recognized from his childhood, one he used to hum to himself when he was afraid, and it was accompanied by a voice, a familiar voice, one he heard every day.

It was his own.

-----

When he next opened his eyes, he wasn't John Sheppard, Air Force pilot. He also wasn't The Mathematician. He was the one, and the same, and he had a TARDIS to fix.

Then, he would have to figure out what to do with the humans. They couldn't stay on his Atlantis, although he might keep Rodney around. He'd make for a rather interesting companion, especially if he introduced him to the Doctor. It seemed like the Doctor was rubbing off on him, first the gift of that rotary telephone, then the tendency to get into trouble, and now a desire to collect companions.

At least Rodney would keep things from getting too boring.

-----

The Doctor froze mid-step as he darted around his TARDIS console, hearing something that he hadn't heard for years.

The Vortex was singing his song, but it was also singing something else, a song he hadn't heard since before the Time War.

He talked about it with Amy once, about how the Vortex sang as Time Lords travelled through it, and about how his song was the only one left.

"Sweetie? What's wrong?" River asked as she leaned against the console, her head tilted curiously. She could tell something had changed, but she couldn't quite put her finger on what. It was just on the tip of her tongue...

The Doctor turned to look at River, his eyes wide, as a large grin erupted across his face.

"I'm not alone!"

It was then that River realized what was different, although she was not quite sure why.

-----

He held on tight to Atlantis' console as she jerked, entering the Vortex for the first time in millennia. It had taken him a long, long time to detach the Alterran technology completely, and Atlantis was now functioning independently. He'd also had to replace numerous circuits and wires and other fiddly bits, many of which he'd been forced to create on his own with items scavenged from the other members of the Atlantis Expedition or retrieved while on missions to other planets. She wasn't completely fixed, not really, but she was healing.

He tilted his head back as the songs of the Vortex washed over him, his brow furrowing a bit when he realized that he could only hear two songs. Never had the Vortex only sang two songs at once – in his last travels, even short trips through the Vortex had given him a headache from all the singing.

Even when he had entered the Vortex, he had not been sure what his next step was going to be. He was much too used to flying by the seat of his pants. His first stop would be to the San Francisco Bay, where he would jettison the Alterran shell of Atlantis in the San Francisco Bay, along with the members of the Atlantis Expedition. They would be fine; the shell was perfectly capable of floating on its own.

Then he was going to call a Doctor to find out what the hell had happened to the other Time Lords.

The rest? Well. He'd just have to think it up as he went along.

Chapter End Notes:Prompt: "Sheppard is actually a Time Lord, and Atlantis is his TARDIS".

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